def test_damprep(self):
tconfig.setup(key, xyz, dloop=True)
n = len(tconfig.r_list)
for i in range(n):
dmpikr = damping.damprep(tconfig.r_list[i], tconfig.r2_list[i],
tconfig.rr1_list[i], tconfig.rr3_list[i],
tconfig.rr5_list[i], tconfig.rr7_list[i],
tconfig.rr9_list[i], 9,
tconfig.dmppri_list[i],
tconfig.dmpprk_list[i])
self.assertListEqual(list(np.round(kdmpikr[i], 5)),
list(np.round(list(dmpikr), 5)))
def uTu_rep(ATOMID, uind=[]):
n = len(ATOMID)
rep = 0
# calculate u*gamma*u
for i in range(n - 1):
if len(uind) != 0:
uix = uind[0, i]
uiy = uind[1, i]
uiz = uind[2, i]
else:
uix = ATOMID[i].uind[0]
uiy = ATOMID[i].uind[1]
uiz = ATOMID[i].uind[2]
xi = ATOMID[i].coordinates[0]
yi = ATOMID[i].coordinates[1]
zi = ATOMID[i].coordinates[2]
sizi = ATOMID[i].sizpr
dmpi = ATOMID[i].dmppr
vali = ATOMID[i].elepr
rscale = ATOMID[i].returnrscale(ATOMID)
# evaluate all sites within the cutoff distance
for k in range(i + 1, n):
xr = ATOMID[k].coordinates[0] - xi
yr = ATOMID[k].coordinates[1] - yi
zr = ATOMID[k].coordinates[2] - zi
r2 = xr**2 + yr**2 + zr**2
r = np.sqrt(r2)
if len(uind) != 0:
ukx = uind[0, k]
uky = uind[1, k]
ukz = uind[2, k]
else:
ukx = ATOMID[k].uind[0]
uky = ATOMID[k].uind[1]
ukz = ATOMID[k].uind[2]
uik = uix * ukx + uiy * uky + uiz * ukz
uir = uix * xr + uiy * yr + uiz * zr
ukr = ukx * xr + uky * yr + ukz * zr
sizk = ATOMID[k].sizpr
dmpk = ATOMID[k].dmppr
valk = ATOMID[k].elepr
term2ik = uik
term3ik = -uir * ukr
rr1 = 1.0 / r
rr3 = rr1 / r2
rr5 = 3.0 * rr3 / r2
rr7 = 5.0 * rr5 / r2
rr9 = 7.0 * rr7 / r2
dmpik = damping.damprep(r, r2, rr1, rr3, rr5, rr7, rr9, 9, dmpi,
dmpk)
e = term2ik * dmpik[2] + term3ik * dmpik[4]
sizik = sizi * sizk
e = sizik * e * rr1 * rscale[k]
if e != 0.:
rep = rep + 2 * e
return rep
def erepel3a(ATOMID, uind=[], dipole=False):
# "erepel3a" calculates the Pauli repulsion energy and also
# partitions the energy among the atoms using a double loop
# zero out the repulsion energy and partitioning terms
if 'exchange-1' in config.param_dict.keys():
dipole = True
n = len(ATOMID)
ner = 0
er = 0.0
einter = 0
aer = np.zeros(n)
# calculate the Pauli repulsion interaction energy term
for i in range(n - 1):
xi = ATOMID[i].coordinates[0]
yi = ATOMID[i].coordinates[1]
zi = ATOMID[i].coordinates[2]
sizi = ATOMID[i].sizpr
dmpi = ATOMID[i].dmppr
vali = ATOMID[i].elepr
ci = ATOMID[i].rpole[0]
dix = ATOMID[i].rpole[1]
diy = ATOMID[i].rpole[2]
diz = ATOMID[i].rpole[3]
if len(uind) != 0:
dix = dix + uind[0, i]
diy = diy + uind[1, i]
diz = diz + uind[2, i]
elif dipole:
dix = dix + ATOMID[i].uind[0]
diy = diy + ATOMID[i].uind[1]
diz = diz + ATOMID[i].uind[2]
qixx = ATOMID[i].rpole[4]
qixy = ATOMID[i].rpole[5]
qixz = ATOMID[i].rpole[6]
qiyy = ATOMID[i].rpole[8]
qiyz = ATOMID[i].rpole[9]
qizz = ATOMID[i].rpole[12]
# set exclusion coefficients for connected atoms
rscale = ATOMID[i].returnrscale(ATOMID)
for k in range(i + 1, n):
xr = ATOMID[k].coordinates[0] - xi
yr = ATOMID[k].coordinates[1] - yi
zr = ATOMID[k].coordinates[2] - zi
r2 = xr * xr + yr * yr + zr * zr
r = np.sqrt(r2)
sizk = ATOMID[k].sizpr
dmpk = ATOMID[k].dmppr
valk = ATOMID[k].elepr
ck = ATOMID[k].rpole[0]
dkx = ATOMID[k].rpole[1]
dky = ATOMID[k].rpole[2]
dkz = ATOMID[k].rpole[3]
if len(uind) != 0:
dkx = dkx + uind[0, k]
dky = dky + uind[1, k]
dkz = dkz + uind[2, k]
elif dipole:
dkx = dkx + ATOMID[k].uind[0]
dky = dky + ATOMID[k].uind[1]
dkz = dkz + ATOMID[k].uind[2]
qkxx = ATOMID[k].rpole[4]
qkxy = ATOMID[k].rpole[5]
qkxz = ATOMID[k].rpole[6]
qkyy = ATOMID[k].rpole[8]
qkyz = ATOMID[k].rpole[9]
qkzz = ATOMID[k].rpole[12]
# intermediates involving moments and separation distance
dir_ = dix * xr + diy * yr + diz * zr
qix = qixx * xr + qixy * yr + qixz * zr
qiy = qixy * xr + qiyy * yr + qiyz * zr
qiz = qixz * xr + qiyz * yr + qizz * zr
qir = qix * xr + qiy * yr + qiz * zr
dkr = dkx * xr + dky * yr + dkz * zr
qkx = qkxx * xr + qkxy * yr + qkxz * zr
qky = qkxy * xr + qkyy * yr + qkyz * zr
qkz = qkxz * xr + qkyz * yr + qkzz * zr
qkr = qkx * xr + qky * yr + qkz * zr
dik = dix * dkx + diy * dky + diz * dkz
qik = qix * qkx + qiy * qky + qiz * qkz
diqk = dix * qkx + diy * qky + diz * qkz
dkqi = dkx * qix + dky * qiy + dkz * qiz
qiqk = 2.0 * (qixy * qkxy + qixz * qkxz + qiyz *
qkyz) + qixx * qkxx + qiyy * qkyy + qizz * qkzz
# get reciprocal distance terms for this interaction
rr1 = 1.0 / r
rr3 = rr1 / r2
rr5 = 3.0 * rr3 / r2
rr7 = 5.0 * rr5 / r2
rr9 = 7.0 * rr7 / r2
# get damping coefficients for the Pauli repulsion energy
dmpik = damping.damprep(r, r2, rr1, rr3, rr5, rr7, rr9, 9, dmpi,
dmpk)
# compute the Pauli repulsion energy for this interaction
term1 = vali * valk
term2 = valk * dir_ - vali * dkr + dik
term3 = vali*qkr + valk*qir - dir_*dkr \
+ 2.0*(dkqi-diqk+qiqk)
term4 = dir_ * qkr - dkr * qir - 4.0 * qik
term5 = qir * qkr
eterm = term1*dmpik[0] + term2*dmpik[2] \
+ term3*dmpik[4] + term4*dmpik[6] \
+ term5*dmpik[8]
sizik = sizi * sizk
e = sizik * rscale[k] * eterm * rr1
# increment the overall Pauli repulsion energy component
if e != 0.0:
ner = ner + 1
er = er + e
aer[i] = aer[i] + 0.5 * e
aer[k] = aer[k] + 0.5 * e
if ATOMID[k].index not in ATOMID[i].connectivity:
einter = einter + e
return er, einter, ner
def rfield0m(ATOMID):
'''rfield0m computes the field due to permanent repulsion'''
n = len(ATOMID)
field = np.zeros((3, n))
# fieldp = np.zeros((3, n))
# find the electrostatic field due to permanent multipoles
for i in range(n - 1):
xi = ATOMID[i].coordinates[0]
yi = ATOMID[i].coordinates[1]
zi = ATOMID[i].coordinates[2]
sizi = ATOMID[i].sizpr
dmpi = ATOMID[i].dmppr
vali = ATOMID[i].elepr
ci = ATOMID[i].rpole[0]
dix = ATOMID[i].rpole[1]
diy = ATOMID[i].rpole[2]
diz = ATOMID[i].rpole[3]
qixx = ATOMID[i].rpole[4]
qixy = ATOMID[i].rpole[5]
qixz = ATOMID[i].rpole[6]
qiyy = ATOMID[i].rpole[8]
qiyz = ATOMID[i].rpole[9]
qizz = ATOMID[i].rpole[12]
# set exclusion coefficients for connected atoms
rscale = ATOMID[i].returnrscale(ATOMID)
for k in range(i + 1, n):
xr = ATOMID[k].coordinates[0] - xi
yr = ATOMID[k].coordinates[1] - yi
zr = ATOMID[k].coordinates[2] - zi
r2 = xr**2 + yr**2 + zr**2
r = np.sqrt(r2)
sizk = ATOMID[k].sizpr
dmpk = ATOMID[k].dmppr
valk = ATOMID[k].elepr
ck = ATOMID[k].rpole[0]
dkx = ATOMID[k].rpole[1]
dky = ATOMID[k].rpole[2]
dkz = ATOMID[k].rpole[3]
qkxx = ATOMID[k].rpole[4]
qkxy = ATOMID[k].rpole[5]
qkxz = ATOMID[k].rpole[6]
qkyy = ATOMID[k].rpole[8]
qkyz = ATOMID[k].rpole[9]
qkzz = ATOMID[k].rpole[12]
# intermediates involving moments and separation distance
dir_ = dix * xr + diy * yr + diz * zr
qix = qixx * xr + qixy * yr + qixz * zr
qiy = qixy * xr + qiyy * yr + qiyz * zr
qiz = qixz * xr + qiyz * yr + qizz * zr
qir = qix * xr + qiy * yr + qiz * zr
dkr = dkx * xr + dky * yr + dkz * zr
qkx = qkxx * xr + qkxy * yr + qkxz * zr
qky = qkxy * xr + qkyy * yr + qkyz * zr
qkz = qkxz * xr + qkyz * yr + qkzz * zr
qkr = qkx * xr + qky * yr + qkz * zr
# get reciprocal distance terms for this interaction
rr1 = 1.0 / r
rr3 = rr1 / r2
rr5 = 3.0 * rr3 / r2
rr7 = 5.0 * rr5 / r2
rr9 = 7.0 * rr7 / r2
dmpik = damping.damprep(r, r2, rr1, rr3, rr5, rr7, rr9, 9, dmpi,
dmpk)
# rr1ik = dmpik[0]*rr1
rr3ik = dmpik[2] * rr3
rr5ik = dmpik[4] * rr5
rr7ik = dmpik[6] * rr7
fid = np.empty(3)
fkd = np.empty(3)
fid[0] = (-xr*(dmpik[2]*valk \
- dmpik[4]*dkr + dmpik[6]*qkr) \
- dmpik[2]*dkx + 2.0*dmpik[4]*qkx)*rr1
fid[1] = (-yr*(dmpik[2]*valk \
- dmpik[4]*dkr + dmpik[6]*qkr) \
- dmpik[2]*dky + 2.0*dmpik[4]*qky)*rr1
fid[2] = (-zr*(dmpik[2]*valk \
- dmpik[4]*dkr + dmpik[6]*qkr) \
- dmpik[2]*dkz + 2.0*dmpik[4]*qkz)*rr1
fkd[0] = (xr*(dmpik[2]*vali \
+ dmpik[4]*dir_ + dmpik[6]*qir) \
- dmpik[2]*dix - 2.0*dmpik[4]*qix)*rr1
fkd[1] = (yr*(dmpik[2]*vali \
+ dmpik[4]*dir_ + dmpik[6]*qir) \
- dmpik[2]*diy - 2.0*dmpik[4]*qiy)*rr1
fkd[2] = (zr*(dmpik[2]*vali \
+ dmpik[4]*dir_ + dmpik[6]*qir) \
- dmpik[2]*diz - 2.0*dmpik[4]*qiz)*rr1
fid[0] = fid[0] * sizk
fid[1] = fid[1] * sizk
fid[2] = fid[2] * sizk
fkd[0] = fkd[0] * sizi
fkd[1] = fkd[1] * sizi
fkd[2] = fkd[2] * sizi
for j in range(3):
field[j, i] = field[j, i] + fid[j] * rscale[k]
field[j, k] = field[j, k] + fkd[j] * rscale[k]
# fieldp[j,i] = fieldp[j,i] + fid[j]*rscale[k]
# fieldp[j,k] = fieldp[j,k] + fkd[j]*rscale[k]
# return field, fieldp
return field